UW Medicine Virology Lab is on close watch for omicron

Monday, December 6, 2021

Pavitra Roychoudhury UW Med
Researchers at the UW School of Medicine’s Virology Laboratory think the omicron variant of COVID-19 will inevitably be detected in larger amounts locally. 
“It's at a pretty low frequency right now, given that we haven't picked up many samples from the last couple of weeks," says Pavitra Roychoudhury, instructor and research associate of Laboratory Medicine at UW Medicine. 

"I think it's a matter of time, given how connected the world is and given how much travel has been occurring over the last few weeks and months.”

Roychoudhury heads genomic sequencing, the process of determining the approximately 30,000-letter pattern of the virus’ genome in a positive COVID-19 test sample. 

This process detected the local presence of the Delta and other variants. UW Medicine’s Virology Lab has the capacity to sequence 2,000 test samples per week. The lab can also screen for a particular mutation found in the Omicron variant, and increase efforts to spot it. 

Monitoring the rate of omicron-positive samples over the coming weeks and months will be important to help researchers determine just how transmissible the variant is, Rouchoudry says. 

“Our ability to sequence a large number of samples every week has certainly bolstered the confidence that we will continue to find this variant. We’re in a much better place in terms of just our ability to find these variants in our lab. And, I think this is similarly true for labs across the country and across the world. 
Having said that, there’s also a lot of disparity in both genomic surveillance as well as vaccination across the globe.”

Roychoudhury notes that, even at a world-class research medical center, we remain a bit behind the virus’ spread. When a person receives the PCR test result, it is just indicating whether or not the COVID virus is present. In order to determine which variant is present, the best method is by sequencing the viral genome and that multi-step process takes time. 

The process of comparing a sample viral genome to others and concluding whether or not it is the omicron variant and what mutations are in that genome can take three or more days and is highly-batched process. That leads to the time lag in most labs.

It should be remembered that even though we are hearing about the new omicron variant, 99.9% of all sequences remain delta. 
Delta is the formidable virus and we need to remember that. 

While there may be some panic about potential new variants in the future, the one that is currently widely spread in the general population is what needs to be dealt with. And right now, that is delta.

Roychoudhury explained that the key to preventing highly transmissible and potentially lethal variants from emerging in the future is by continuing the practices that have been successful during the course of the pandemic. Masking and social distancing will continue to be the best line of defense.


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